Merge pull request #365 from K3D-tools/devel

2.14.5
K3D-tools · Jul 26, 2022 · 2b1cf61 · 2b1cf61
2 parents b948361 + ecee975
commit 2b1cf61
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diff --git a/docs/source/reference/assets/factory/mask.mhd b/docs/source/reference/assets/factory/mask.mhd
@@ -0,0 +1,14 @@
+ObjectType = Image
+NDims = 3
+BinaryData = True
+BinaryDataByteOrderMSB = False
+CompressedData = True
+CompressedDataSize = 809269
+TransformMatrix = 1 0 0 0 1 0 0 0 1
+Offset = -83.319299999999998 -245.31899999999999 -206.19999999999999
+CenterOfRotation = 0 0 0
+AnatomicalOrientation = RAI
+ElementSpacing = 0.36132799999999998 0.36132799999999998 0.5
+DimSize = 512 512 317
+ElementType = MET_SHORT
+ElementDataFile = mask.zraw
diff --git a/docs/source/reference/assets/factory/mask.zraw b/docs/source/reference/assets/factory/mask.zraw
diff --git a/docs/source/reference/factory.mip.rst b/docs/source/reference/factory.mip.rst
@@ -62,4 +62,38 @@ Colormap
     plot.display()
 
 .. k3d_plot ::
-  :filename: plots/factory/mip_colormap_plot.py
+  :filename: plots/factory/mip_colormap_plot.py
+
+
+Mask
+^^^^
+
+:download:`heart.mhd <./assets/factory/heart.mhd>`
+:download:`heart.zraw <./assets/factory/heart.zraw>`
+:download:`heart.mhd <./assets/factory/mask.mhd>`
+:download:`heart.zraw <./assets/factory/mask.zraw>`
+
+.. code-block:: python3
+
+    import k3d
+    import numpy as np
+    import SimpleITK as sitk
+
+    im_sitk = sitk.ReadImage('heart.mhd')
+    img = sitk.GetArrayFromImage(im_sitk)
+
+    mask_sitk = sitk.ReadImage('mask.mhd')
+    mask = sitk.GetArrayFromImage(mask_sitk)
+
+    plt_mip = k3d.mip(img.astype(np.float32),
+                      mask=mask.astype(np.uint8),
+                      mask_opacities=[0.025, 3.0],
+                      color_range=[0, 700])
+
+    plot = k3d.plot()
+    plot += plt_mip
+    plot.display()
+
+.. k3d_plot ::
+    :filename: plots/factory/mip_mask_plot.py
+
diff --git a/docs/source/reference/factory.volume.rst b/docs/source/reference/factory.volume.rst
@@ -62,4 +62,37 @@ Colormap
     plot.display()
 
 .. k3d_plot ::
-    :filename: plots/factory/volume_colormap_plot.py
+    :filename: plots/factory/volume_colormap_plot.py
+
+Mask
+^^^^
+
+:download:`heart.mhd <./assets/factory/heart.mhd>`
+:download:`heart.zraw <./assets/factory/heart.zraw>`
+:download:`heart.mhd <./assets/factory/mask.mhd>`
+:download:`heart.zraw <./assets/factory/mask.zraw>`
+
+.. code-block:: python3
+
+    import k3d
+    import numpy as np
+    import SimpleITK as sitk
+
+    im_sitk = sitk.ReadImage('heart.mhd')
+    img = sitk.GetArrayFromImage(im_sitk)
+
+    mask_sitk = sitk.ReadImage('mask.mhd')
+    mask = sitk.GetArrayFromImage(mask_sitk)
+
+    plt_volume = k3d.volume(img.astype(np.float32),
+                            mask=mask.astype(np.uint8),
+                            mask_opacities=[0.025, 3.0],
+                            color_range=[0, 700])
+
+    plot = k3d.plot()
+    plot += plt_volume
+    plot.display()
+
+.. k3d_plot ::
+  :filename: plots/factory/volume_mask_plot.py
+
diff --git a/docs/source/reference/plots/factory/mip_mask_plot.py b/docs/source/reference/plots/factory/mip_mask_plot.py
@@ -0,0 +1,31 @@
+import SimpleITK as sitk
+import numpy as np
+import os
+
+import k3d
+
+
+def generate():
+    filepath = os.path.join(os.path.abspath(os.path.dirname(__file__)),
+                            '../../assets/factory/heart.mhd')
+
+    im_sitk = sitk.ReadImage(filepath)
+    img = sitk.GetArrayFromImage(im_sitk)
+
+    filepath = os.path.join(os.path.abspath(os.path.dirname(__file__)),
+                            '../../assets/factory/mask.mhd')
+
+    mask_sitk = sitk.ReadImage(filepath)
+    mask = sitk.GetArrayFromImage(mask_sitk)
+
+    plt_mip = k3d.mip(img.astype(np.float32),
+                      mask=mask.astype(np.uint8),
+                      mask_opacities=[0.025, 3.0],
+                      color_range=[0, 700])
+
+    plot = k3d.plot()
+    plot += plt_mip
+
+    plot.snapshot_type = 'inline'
+
+    return plot.get_snapshot()
diff --git a/docs/source/reference/plots/factory/volume_mask_plot.py b/docs/source/reference/plots/factory/volume_mask_plot.py
@@ -0,0 +1,30 @@
+import SimpleITK as sitk
+import numpy as np
+import os
+
+import k3d
+
+
+def generate():
+    filepath = os.path.join(os.path.abspath(os.path.dirname(__file__)),
+                            '../../assets/factory/heart.mhd')
+
+    im_sitk = sitk.ReadImage(filepath)
+    img = sitk.GetArrayFromImage(im_sitk)
+
+    filepath = os.path.join(os.path.abspath(os.path.dirname(__file__)),
+                            '../../assets/factory/mask.mhd')
+
+    mask_sitk = sitk.ReadImage(filepath)
+    mask = sitk.GetArrayFromImage(mask_sitk)
+
+    plt_volume = k3d.volume(img.astype(np.float32),
+                            mask=mask.astype(np.uint8),
+                            mask_opacities=[0.025, 3.0],
+                            color_range=[0, 700])
+
+    plot = k3d.plot()
+    plot += plt_volume
+
+    plot.snapshot_type = 'inline'
+    return plot.get_snapshot()
diff --git a/js/Gruntfile.js b/js/Gruntfile.js
@@ -8,77 +8,77 @@ module.exports = function (grunt) {
 
     grunt.initConfig({
         webpack: {
-            myConfig: webpackConfig
+            myConfig: webpackConfig,
         },
         eslint: {
             options: {
-                config: '.eslintrc.js'
+                config: '.eslintrc.js',
             },
-            target: ['src/core/*.js']
+            target: ['src/core/*.js'],
         },
         watch: {
             webpack: {
                 files: [
                     'src/**/*.js',
                     'src/**/*.glsl',
-                    'src/**/*.css'
+                    'src/**/*.css',
                 ],
                 tasks: ['webpack'],
                 options: {
-                    livereload: true
-                }
+                    livereload: true,
+                },
             },
             development: {
                 files: [
-                    'development.html'
+                    'development.html',
                 ],
                 options: {
-                    livereload: true
-                }
-            }
+                    livereload: true,
+                },
+            },
         },
         connect: {
             server: {
                 options: {
                     port: 9000,
-                    base: './'
-                }
-            }
+                    base: './',
+                },
+            },
         },
         jsdoc: {
             dist: {
                 src: ['src/providers/**/*.js', 'src/core/**/*.js'],
                 options: {
                     destination: 'doc',
-                    readme: 'README.md'
-                }
-            }
+                    readme: 'README.md',
+                },
+            },
         },
         open: {
             dev: {
-                path: 'http://localhost:9000/development.html'
-            }
+                path: 'http://localhost:9000/development.html',
+            },
         },
         clean: {
             doc: 'doc',
             dist: 'dist',
-            dev: 'dev'
-        }
+            dev: 'dev',
+        },
     });
 
     grunt.registerTask('codeStyle', [
-        'eslint'
+        'eslint',
     ]);
 
     grunt.registerTask('doc', [
         'clean:doc',
-        'jsdoc'
+        'jsdoc',
     ]);
 
     grunt.registerTask('build', () => {
         grunt.task.run([
             'clean',
-            'webpack'
+            'webpack',
         ]);
     });
 
@@ -88,7 +88,7 @@ module.exports = function (grunt) {
             'webpack',
             'connect',
             'open:dev',
-            'watch'
+            'watch',
         ]);
     });
 };